X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=ff5c1b0944aac1516cee9e12936b0b524d5d89d8;hb=d0771875f23ab994c4f85fb6cd604378768df10e;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index e18e273..ff5c1b0 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,18 +1,99 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Sequence Fetcher + + +

+ Sequence Fetcher +

+

+ Jalview can retrieve sequences from certain databases using either + the DBFetch service provided by the EMBL European Bioinformatics + Institute, or, since Jalview 2.4, DAS servers capable of the sequence + command (configured in DAS settings). +

+ The Jalview Sequence Fetcher Dialog Box +

The Sequence Fetcher dialog box can be opened via the + "File" menu on the main desktop in order to retrieve + sequences as a new alignment, or opened via the "File" + menu of an existing alignment to import additional sequences. There + may be a short delay when the sequence fetcher is first opened, + whilst Jalview compiles the list of available sequence datasources + from the currently defined DAS server registry.

+

+ First, select the database you want to retrieve + sequences from by clicking the button labeled 'Select database + retrieval source'. If a database source is already selected, then + the button's label will change to show the currently selected + database. +

+ Database selection dialog for fetching sequences (introduced in Jalview 2.8) +

Since Jalview 2.8, the available databases are shown as a tree + in a popup dialog box. The databases are ordered alphabetically, and + if there are many sources for the same type of sequence identifier, + they will be grouped together in a sub-branch branch labeled with + the identifier.

+

+ Once you have selected the sequence database using the popup dialog + box, enter one or more accession ids (as a + semi-colon separated list), or press the "Example" button + to paste the example accession for the currently selected database + into the retrieval box. Finally, press "OK" to initiate + the retrieval. +

+

+ Fetching from The PDB with the EMBL-EBI PDBe Search + Interface +

+

+ Since Jalview 2.9, selecting PDB as the sequence database will open + the PDB Sequence Fetcher for + discovering and retrieving structures. +

+

+ Only retrieving part of a sequence +

+

+ DAS sources (indicated by a "(DAS)") allow a + range to be specified in addition to a sequence ID. To retrieve 50 + residues starting at position 35 in UNIPROT sequence P73137 using + the UNIPROT DAS server, you would enter "'P73137:35,84'.
+ Full support for DAS range queries was introduced in + Jalview 2.8 +

+ +

If you use the WSDBFetch sequence fetcher services (EMBL, + UniProt, PFAM, and RFAM) in work for publication, please cite:

+

+ Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate + J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez + R.
SOAP-based services provided by the European + Bioinformatics Institute.
Nucleic Acids Res. 33(1):W25-W28 + (2005)

+

+ +